994049f75b593264f0ff047f88903468bf1c2031
jeltje.van.baren
  Fri Apr 4 13:35:35 2025 -0700
mm10 and hg38 encode4

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index af6e055ba93..62e197a744f 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -19472,15 +19472,61 @@
     \
    -target2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \
    GCF_016772045.2 mm10) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	190m23.152s
 
     sed -e 's/^/    # /;' fb.GCF_016772045.2.chainRBest.Mm10.txt
     # 658848325 bases of 2654063983 (24.824%) in intersection
 
 real	663m45.533s
 user	0m3.053s
 sys	0m2.728s
 ##############################################################################
+##############################################################################
+# ENCODE4 triplets - Jeltje April 2025
+
+mkdir -p april2025
+#wget -O april2025/mouse_ucsc_transcripts.gtf "https://zenodo.org/records/15116042/files/mouse_ucsc_transcripts.gtf?download=1"
+#wget -O  april2025/filt_ab_tpm_mouse.tsv "https://zenodo.org/records/15116042/files/filt_ab_tpm_mouse.tsv?download=1"
+#wget -O  april2025/mouse_protein_summary.tsv "https://zenodo.org/records/15116042/files/mouse_protein_summary.tsv?download=1"
+#wget -O  april2025/mouse_sample_info.tsv https://zenodo.org/records/15116042/files/lr_mouse_library_data_summary.tsv?download=1
+
+gtfFile='april2025/mouse_ucsc_transcripts.gtf'
+quantFile='april2025/filt_ab_tpm_mouse.tsv'  # really counts per million since every read is full length
+protFile='april2025/mouse_protein_summary.tsv'
+sampleFile='april2025/mouse_sample_info.tsv'
+# this outputs bed12 + extra ID fields, topval expressions for mouseover and an expression html table
+./gtfToBed.py $gtfFile $quantFile $protFile $sampleFile transcripts.bed > missing.ids
+bedSort transcripts.bed transcripts.bed 
+
+cat << '_EOF_' > encode4.as
+table encode4
+"Bed 12+8 file with annotation source and values per sample in a html table."
+    (
+    string chrom;      "Chromosome (or contig, scaffold, etc.)"
+    uint   chromStart; "Start position in chromosome"
+    uint   chromEnd;   "End position in chromosome"
+    string name;       "Name of item"
+    uint   score;      "Score from 0-1000"
+    char[1] strand;    "+ or -"
+    uint thickStart;   "Start of where display should be thick (start codon)"
+    uint thickEnd;     "End of where display should be thick (stop codon)"
+    uint reserved;     "Used as itemRgb as of 2004-11-22"
+    int blockCount;    "Number of blocks"
+    int[blockCount] blockSizes; "Comma separated list of block sizes"
+    int[blockCount] chromStarts; "Start positions relative to chromStart"
+    string source;      "Annotation source"
+    string gene_id;     "gene ID"	
+    string gene_name;   "gene name"	
+    string transcript_id;   "transcript ID"	
+    string transcript_name;   "transcript name"	
+    float maxScore;   "Highest expression score (counts per million)"
+    lstring maxScoreHtml;   "Highest expression score and sample(s)"
+    lstring expr_table; "Expression values per sample in TPM"
+    )
+_EOF_
+
+bedToBigBed -type=bed12+8 -as=encode4.as -tab transcripts.bed /hive/data/genomes/mm10/chrom.sizes encode4.bb
+